Genome-Wide Association Analysis Identifies Genomic Regions and Candidate Genes for Growth and Fatness Traits in Diannan Small-Ear (DSE) Pigs

SIMPLE SUMMARY: Growth and fatness traits are economically important in pig farming. The exploration of underlying genetic architecture for vital phenotypes is helpful in speeding up the process of genetic improvement for different pig breeds. Hence, for Diannan small-ear (DSE) pig, eight phenotypic traits including six body measurement traits and two fatness traits were examined. Based on the Geneseek Porcine 50K SNP Chip data, single nucleotide polymorphisms (SNPs) were detected in a DSE pig population. Through a genome-wide association study, some candidate genes were detected potentially related to the traits of interest. These findings help to understand the genetic basis of porcine growth traits could be used in future pig breeding schemes. ABSTRACT: In the livestock industry, the growth and fatness traits are directly related to production efficiency and economic profits. As for Diannan small-ear (DSE) pigs, a unique indigenous breed, the genetic architecture of growth and fatness traits is still elusive. The aim of this study was to search the genetic loci and candidate genes associated with phenotypic traits in DSE pigs using GWAS based on the Geneseek Porcine 50K SNP Chip data. A total of 22,146 single nucleotide polymorphisms (SNPs) were detected in 265 DSE pigs and used for Genome-wide association studies (GWAS) analysis. Seven SNPs were found to be associated with back height, chest circumference, cannon bone circumference, and backfat thickness at the suggestive significance level. Based on gene annotation results, these seven SNPs were, respectively, mapped to the following candidate genes, VIPR2, SLC10A2, NUCKS1, MCT1, CHCHD3, SMOX, and GPR1, which are mainly involved with adipocyte differentiation, lipid metabolism, skeletal muscle development, and average daily weight gain. Our work offers novel insights into the genetic architecture of economically important traits in swine and may play an important role in breeding using molecular markers in the DSE breed.